TASK-5964 - Clinical Improvements

opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/AnalysisClinicalCommandExecutor.java

@@ -347,7 +347,7 @@ private RestResponse<ClinicalAnalysis> create() throws Exception {
             putNestedIfNotEmpty(beanParams, "disorder.id", commandOptions.disorderId, true);
             putNestedIfNotEmpty(beanParams, "proband.id", commandOptions.probandId, true);
             putNestedIfNotEmpty(beanParams, "family.id", commandOptions.familyId, true);
-            putNestedIfNotNull(beanParams, "panelLock", commandOptions.panelLock, true);
+            putNestedIfNotNull(beanParams, "panelLocked", commandOptions.panelLocked, true);
             putNestedIfNotEmpty(beanParams, "analyst.id", commandOptions.analystId, true);
             putNestedIfNotEmpty(beanParams, "report.title", commandOptions.reportTitle, true);
             putNestedIfNotEmpty(beanParams, "report.overview", commandOptions.reportOverview, true);
@@ -367,6 +367,7 @@ private RestResponse<ClinicalAnalysis> create() throws Exception {
             putNestedIfNotEmpty(beanParams, "responsible.address", commandOptions.responsibleAddress, true);
             putNestedIfNotEmpty(beanParams, "responsible.city", commandOptions.responsibleCity, true);
             putNestedIfNotEmpty(beanParams, "responsible.postcode", commandOptions.responsiblePostcode, true);
+            putNestedIfNotEmpty(beanParams, "interpretation.name", commandOptions.interpretationName, true);
             putNestedIfNotEmpty(beanParams, "interpretation.description", commandOptions.interpretationDescription, true);
             putNestedIfNotEmpty(beanParams, "interpretation.clinicalAnalysisId", commandOptions.interpretationClinicalAnalysisId, true);
             putNestedIfNotEmpty(beanParams, "interpretation.creationDate", commandOptions.interpretationCreationDate, true);
@@ -419,6 +420,7 @@ private RestResponse<ObjectMap> distinct() throws Exception {
         queryParams.putIfNotEmpty("dueDate", commandOptions.dueDate);
         queryParams.putIfNotEmpty("qualityControlSummary", commandOptions.qualityControlSummary);
         queryParams.putIfNotEmpty("release", commandOptions.release);
+        queryParams.putIfNotNull("snapshot", commandOptions.snapshot);
         queryParams.putIfNotEmpty("status", commandOptions.status);
         queryParams.putIfNotEmpty("internalStatus", commandOptions.internalStatus);
         queryParams.putIfNotEmpty("annotation", commandOptions.annotation);
@@ -439,6 +441,7 @@ private RestResponse<ObjectMap> distinctInterpretation() throws Exception {
         queryParams.putIfNotEmpty("study", commandOptions.study);
         queryParams.putIfNotEmpty("id", commandOptions.id);
         queryParams.putIfNotEmpty("uuid", commandOptions.uuid);
+        queryParams.putIfNotEmpty("name", commandOptions.name);
         queryParams.putIfNotEmpty("clinicalAnalysisId", commandOptions.clinicalAnalysisId);
         queryParams.putIfNotEmpty("analystId", commandOptions.analystId);
         queryParams.putIfNotEmpty("methodName", commandOptions.methodName);
@@ -471,6 +474,7 @@ private RestResponse<Interpretation> searchInterpretation() throws Exception {
         queryParams.putIfNotEmpty("study", commandOptions.study);
         queryParams.putIfNotEmpty("id", commandOptions.id);
         queryParams.putIfNotEmpty("uuid", commandOptions.uuid);
+        queryParams.putIfNotEmpty("name", commandOptions.name);
         queryParams.putIfNotEmpty("clinicalAnalysisId", commandOptions.clinicalAnalysisId);
         queryParams.putIfNotEmpty("analystId", commandOptions.analystId);
         queryParams.putIfNotEmpty("methodName", commandOptions.methodName);
@@ -1145,6 +1149,7 @@ private RestResponse<ClinicalAnalysis> search() throws Exception {
         queryParams.putIfNotEmpty("dueDate", commandOptions.dueDate);
         queryParams.putIfNotEmpty("qualityControlSummary", commandOptions.qualityControlSummary);
         queryParams.putIfNotEmpty("release", commandOptions.release);
+        queryParams.putIfNotNull("snapshot", commandOptions.snapshot);
         queryParams.putIfNotEmpty("status", commandOptions.status);
         queryParams.putIfNotEmpty("internalStatus", commandOptions.internalStatus);
         queryParams.putIfNotEmpty("annotation", commandOptions.annotation);
@@ -1293,7 +1298,7 @@ private RestResponse<ClinicalAnalysis> update() throws Exception {
             putNestedIfNotEmpty(beanParams, "description", commandOptions.description, true);
             putNestedIfNotNull(beanParams, "type", commandOptions.type, true);
             putNestedIfNotEmpty(beanParams, "disorder.id", commandOptions.disorderId, true);
-            putNestedIfNotNull(beanParams, "panelLock", commandOptions.panelLock, true);
+            putNestedIfNotNull(beanParams, "panelLocked", commandOptions.panelLocked, true);
             putNestedIfNotEmpty(beanParams, "proband.id", commandOptions.probandId, true);
             putNestedIfNotEmpty(beanParams, "family.id", commandOptions.familyId, true);
             putNestedIfNotNull(beanParams, "locked", commandOptions.locked, true);
@@ -1325,6 +1330,7 @@ private RestResponse<ClinicalAnalysis> update() throws Exception {
             putNestedIfNotEmpty(beanParams, "priority.id", commandOptions.priorityId, true);
             putNestedMapIfNotEmpty(beanParams, "attributes", commandOptions.attributes, true);
             putNestedIfNotEmpty(beanParams, "status.id", commandOptions.statusId, true);
+            putNestedIfNotNull(beanParams, "panelLock", commandOptions.panelLock, true);
 
             clinicalAnalysisUpdateParams = JacksonUtils.getDefaultObjectMapper().copy()
                     .configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, true)
@@ -1369,6 +1375,7 @@ private RestResponse<ClinicalAnalysis> info() throws Exception {
         queryParams.putIfNotEmpty("exclude", commandOptions.exclude);
         queryParams.putIfNotNull("flattenAnnotations", commandOptions.flattenAnnotations);
         queryParams.putIfNotEmpty("study", commandOptions.study);
+        queryParams.putIfNotEmpty("version", commandOptions.version);
         queryParams.putIfNotNull("deleted", commandOptions.deleted);
         if (queryParams.get("study") == null && OpencgaMain.isShellMode()) {
             queryParams.putIfNotEmpty("study", sessionManager.getSession().getCurrentStudy());
@@ -1404,6 +1411,7 @@ private RestResponse<Interpretation> createInterpretation() throws Exception {
                     .readValue(new java.io.File(commandOptions.jsonFile), InterpretationCreateParams.class);
         } else {
             ObjectMap beanParams = new ObjectMap();
+            putNestedIfNotEmpty(beanParams, "name", commandOptions.name, true);
             putNestedIfNotEmpty(beanParams, "description", commandOptions.description, true);
             putNestedIfNotEmpty(beanParams, "clinicalAnalysisId", commandOptions.clinicalAnalysisId, true);
             putNestedIfNotEmpty(beanParams, "creationDate", commandOptions.creationDate, true);
@@ -1493,6 +1501,7 @@ private RestResponse<Interpretation> updateInterpretation() throws Exception {
                     .readValue(new java.io.File(commandOptions.jsonFile), InterpretationUpdateParams.class);
         } else {
             ObjectMap beanParams = new ObjectMap();
+            putNestedIfNotEmpty(beanParams, "name", commandOptions.name, true);
             putNestedIfNotEmpty(beanParams, "description", commandOptions.description, true);
             putNestedIfNotEmpty(beanParams, "analyst.id", commandOptions.analystId, true);
             putNestedIfNotEmpty(beanParams, "method.name", commandOptions.methodName, true);

opencga-app/src/main/java/org/opencb/opencga/app/cli/main/options/AnalysisClinicalCommandOptions.java

@@ -241,8 +241,8 @@ public class CreateCommandOptions {
         @Parameter(names = {"--family-id"}, description = "The body web service id parameter", required = false, arity = 1)
         public String familyId;
 
-        @Parameter(names = {"--panel-lock"}, description = "The body web service panelLock parameter", required = false, arity = 1)
-        public Boolean panelLock;
+        @Parameter(names = {"--panel-locked"}, description = "The body web service panelLocked parameter", required = false, arity = 1)
+        public Boolean panelLocked;
 
         @Parameter(names = {"--analyst-id"}, description = "The body web service id parameter", required = false, arity = 1)
         public String analystId;
@@ -301,6 +301,9 @@ public class CreateCommandOptions {
         @Parameter(names = {"--responsible-postcode"}, description = "The body web service postcode parameter", required = false, arity = 1)
         public String responsiblePostcode;
 
+        @Parameter(names = {"--interpretation-name"}, description = "The body web service name parameter", required = false, arity = 1)
+        public String interpretationName;
+
         @Parameter(names = {"--interpretation-description"}, description = "The body web service description parameter", required = false, arity = 1)
         public String interpretationDescription;
 
@@ -423,6 +426,9 @@ public class DistinctCommandOptions {
         @Parameter(names = {"--release"}, description = "Release when it was created", required = false, arity = 1)
         public String release; 
 
+        @Parameter(names = {"--snapshot"}, description = "Snapshot value (Latest version of the entry in the specified release)", required = false, arity = 1)
+        public Integer snapshot; 
+
         @Parameter(names = {"--status"}, description = "Filter by status", required = false, arity = 1)
         public String status; 
 
@@ -455,6 +461,9 @@ public class DistinctInterpretationCommandOptions {
         @Parameter(names = {"--uuid"}, description = "Comma separated list of Interpretation UUIDs up to a maximum of 100", required = false, arity = 1)
         public String uuid; 
 
+        @Parameter(names = {"--name", "-n"}, description = "Comma separated list of Interpretation names up to a maximum of 100", required = false, arity = 1)
+        public String name; 
+
         @Parameter(names = {"--clinical-analysis-id"}, description = "Clinical Analysis id", required = false, arity = 1)
         public String clinicalAnalysisId; 
 
@@ -523,6 +532,9 @@ public class SearchInterpretationCommandOptions {
         @Parameter(names = {"--uuid"}, description = "Comma separated list of Interpretation UUIDs up to a maximum of 100", required = false, arity = 1)
         public String uuid; 
 
+        @Parameter(names = {"--name", "-n"}, description = "Comma separated list of Interpretation names up to a maximum of 100", required = false, arity = 1)
+        public String name; 
+
         @Parameter(names = {"--clinical-analysis-id"}, description = "Clinical Analysis id", required = false, arity = 1)
         public String clinicalAnalysisId; 
 
@@ -1740,6 +1752,9 @@ public class SearchCommandOptions {
         @Parameter(names = {"--release"}, description = "Release when it was created", required = false, arity = 1)
         public String release; 
 
+        @Parameter(names = {"--snapshot"}, description = "Snapshot value (Latest version of the entry in the specified release)", required = false, arity = 1)
+        public Integer snapshot; 
+
         @Parameter(names = {"--status"}, description = "Filter by status", required = false, arity = 1)
         public String status; 
 
@@ -2027,8 +2042,8 @@ public class UpdateCommandOptions {
         @Parameter(names = {"--disorder-id"}, description = "The body web service id parameter", required = false, arity = 1)
         public String disorderId;
 
-        @Parameter(names = {"--panel-lock"}, description = "The body web service panelLock parameter", required = false, arity = 1)
-        public Boolean panelLock;
+        @Parameter(names = {"--panel-locked"}, description = "The body web service panelLocked parameter", required = false, arity = 1)
+        public Boolean panelLocked;
 
         @Parameter(names = {"--proband-id"}, description = "The body web service id parameter", required = false, arity = 1)
         public String probandId;
@@ -2123,6 +2138,9 @@ public class UpdateCommandOptions {
         @Parameter(names = {"--status-id"}, description = "The body web service id parameter", required = false, arity = 1)
         public String statusId;
 
+        @Parameter(names = {"--panel-lock"}, description = "The body web service panelLock parameter", required = false, arity = 1)
+        public Boolean panelLock;
+
     }
 
     @Parameters(commandNames = {"annotation-sets-annotations-update"}, commandDescription ="Update annotations from an annotationSet")
@@ -2172,6 +2190,9 @@ public class InfoCommandOptions {
         @Parameter(names = {"--study", "-s"}, description = "Study [[organization@]project:]study where study and project can be either the ID or UUID", required = false, arity = 1)
         public String study; 
 
+        @Parameter(names = {"--version"}, description = "Comma separated list of clinical versions. 'all' to get all the clinical versions. Not supported if multiple clinical ids are provided", required = false, arity = 1)
+        public String version; 
+
         @Parameter(names = {"--deleted"}, description = "Boolean to retrieve deleted entries", required = false, help = true, arity = 0)
         public boolean deleted = false; 
 
@@ -2207,6 +2228,9 @@ public class CreateInterpretationCommandOptions {
         @Parameter(names = {"--include-result"}, description = "Flag indicating to include the created or updated document result in the response", required = false, help = true, arity = 0)
         public boolean includeResult = false; 
 
+        @Parameter(names = {"--name", "-n"}, description = "The body web service name parameter", required = false, arity = 1)
+        public String name;
+
         @Parameter(names = {"--description"}, description = "The body web service description parameter", required = false, arity = 1)
         public String description;
 
@@ -2344,6 +2368,9 @@ public class UpdateInterpretationCommandOptions {
         @Parameter(names = {"--include-result"}, description = "Flag indicating to include the created or updated document result in the response", required = false, help = true, arity = 0)
         public boolean includeResult = false; 
 
+        @Parameter(names = {"--name", "-n"}, description = "The body web service name parameter", required = false, arity = 1)
+        public String name;
+
         @Parameter(names = {"--description"}, description = "The body web service description parameter", required = false, arity = 1)
         public String description;
 

opencga-app/src/main/java/org/opencb/opencga/app/migrations/v3/v3_2_0/TASK_5964/AddInterpretationName.java

@@ -0,0 +1,35 @@
+package org.opencb.opencga.app.migrations.v3.v3_2_0.TASK_5964;
+
+import com.mongodb.client.model.Filters;
+import com.mongodb.client.model.Projections;
+import com.mongodb.client.model.UpdateOneModel;
+import org.bson.Document;
+import org.bson.conversions.Bson;
+import org.opencb.opencga.catalog.db.mongodb.OrganizationMongoDBAdaptorFactory;
+import org.opencb.opencga.catalog.migration.Migration;
+import org.opencb.opencga.catalog.migration.MigrationTool;
+
+import java.util.Arrays;
+
+@Migration(id = "add_interpretation_name", description = "Add Interpretation name #TASK-5964", version = "3.2.0",
+        language = Migration.MigrationLanguage.JAVA, domain = Migration.MigrationDomain.CATALOG, date = 20240610)
+public class AddInterpretationName extends MigrationTool {
+
+    @Override
+    protected void run() throws Exception {
+        // Add new Interpretation name field
+        Bson nameDoesNotExistQuery = Filters.exists("name", false);
+        Bson projection = Projections.include("id");
+        for (String collection : Arrays.asList(OrganizationMongoDBAdaptorFactory.INTERPRETATION_COLLECTION,
+                OrganizationMongoDBAdaptorFactory.INTERPRETATION_ARCHIVE_COLLECTION,
+                OrganizationMongoDBAdaptorFactory.DELETED_INTERPRETATION_COLLECTION)) {
+            migrateCollection(collection, nameDoesNotExistQuery, projection,
+                    (document, bulk) -> {
+                        Document updateDocument = new Document()
+                                .append("name", document.get("id"));
+                        bulk.add(new UpdateOneModel<>(Filters.eq("_id", document.get("_id")), new Document("$set", updateDocument)));
+                    });
+        }
+    }
+
+}